USeq Source Code

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

Commit [r284] Maximize Restore History

Lots of mods, see the release notes for 8.8.9.

Authored by: biotelerock 2015-02-24

Browse code at this revision

Parent: [r283]

Child: [r285]

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changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
added	/trunk/Source/edu/utah/seq/analysis/MethylationArrayCVScanner.java
changed	/trunk/Source/edu/utah/seq/analysis/MethylationArrayScanner.java
changed	/trunk/Source/edu/utah/seq/analysis/ScanSeqs.java
changed	/trunk/Source/edu/utah/seq/base/BaseClassifier.java
renamed	/trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java -> /trunk/Source/edu/utah/seq/parsers/SamAlignmentExtractor.java
added	/trunk/Source/edu/utah/seq/cnv
added	/trunk/Source/edu/utah/seq/cnv/GeneExonSample.java
added	/trunk/Source/edu/utah/seq/cnv/PoisRegCNV.java
changed	/trunk/Source/edu/utah/seq/data/MethylationArraySamplePair.java
changed	/trunk/Source/edu/utah/seq/data/PointData.java
changed	/trunk/Source/edu/utah/seq/parsers/SamTranscriptomeParser.java
changed	/trunk/Source/edu/utah/seq/useq/data/Region.java
added	/trunk/Source/edu/utah/seq/vcf/AdetexBafVCFParser.java
added	/trunk/Source/edu/utah/seq/vcf/MuTechVCFParser.java
changed	/trunk/Source/edu/utah/seq/vcf/SomaticSniperVCFParser.java
added	/trunk/Source/edu/utah/seq/vcf/StrelkaVCFParser.java
added	/trunk/Source/edu/utah/seq/vcf/VCFNoCallFilter.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFParser.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFSample.java
changed	/trunk/Source/util/apps/FilterIntersectingRegions.java
changed	/trunk/Source/util/bio/annotation/ExonIntron.java
added	/trunk/Source/util/bio/parsers/MergeOverlappingGenes.java
changed	/trunk/Source/util/bio/parsers/UCSCGeneLine.java

/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/MethylationArrayCVScanner.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/MethylationArrayScanner.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/ScanSeqs.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/base/BaseClassifier.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/base/SamAlignmentExtractor.java to /trunk/Source/edu/utah/seq/parsers/SamAlignmentExtractor.java

File was renamed.

/trunk/Source/edu/utah/seq/cnv

Directory.

/trunk/Source/edu/utah/seq/cnv/GeneExonSample.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/cnv/PoisRegCNV.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/data/MethylationArraySamplePair.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/data/PointData.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/SamTranscriptomeParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/useq/data/Region.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/AdetexBafVCFParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/MuTechVCFParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/SomaticSniperVCFParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/StrelkaVCFParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFNoCallFilter.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFSample.java Diff Switch to side-by-side view

/trunk/Source/util/apps/FilterIntersectingRegions.java Diff Switch to side-by-side view

/trunk/Source/util/bio/annotation/ExonIntron.java Diff Switch to side-by-side view

/trunk/Source/util/bio/parsers/MergeOverlappingGenes.java Diff Switch to side-by-side view

/trunk/Source/util/bio/parsers/UCSCGeneLine.java Diff Switch to side-by-side view

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